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Hundreds of highly conserved distal cis-regulatory elements have been characterized to date in vertebrate genomes1. Many thousands more are predicted based on comparative genomics2,3. Yet, in stark contrast to the genes they regulate, virtually none of these regions can be traced using sequence similarity in invertebrates, leaving their evolutionary origin obscure. Here we show that a class of conserved, primarily non-coding regions in tetrapods originated from a novel short interspersed repetitive element (SINE) retroposon family that was active in Sarcopterygii (lobe-finned fishes and terrestrial vertebrates) in the Silurian at least 410 Mya4, and, remarkably, appears to be recently active in the "living fossil" Indonesian coelacanth, Latimeria menadoensis. We show that one copy is a distal enhancer, located 500kb from the neuro-developmental gene ISL1. Several others represent new, possibly regulatory, alternatively spliced exons in the middle of pre-existing Sarcopterygian genes. One of these is the >200bp ultraconserved region5, 100 percent identical in mammals, and 80 percent identical to the coelacanth SINE, that contains a 31aa alternatively spliced exon of the mRNA processing gene PCBP26. These add to a growing list of examples7 in which relics of transposable elements have acquired a function that serves their host, a process termed "exaptation"8, and provide an origin for at least some of the highly-conserved vertebrate-specific genomic sequences recently discovered using comparative genomics.